Table 2.
pT | PRS.full | PRS.no.APOE | PRS.AD | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
N SNPs | AUC (%) | R2 | OR (95% CI) |
N SNPs | AUC (%) | R2 | OR (95% CI) |
AUC (%) |
R2 | OR (95% CI) |
|
APOE(ε2 + ε4) | 2 | 70.0 | 0.18 | 2.2 (1.8,2.7) | – | – | – | – | 70.0 | 0.18 | 2.2 (1.8, 2.7) |
5e-8 | 65 | 69.8 | 0.16 | 2.2 (1.8, 2.7) | 17 | 55.7 | 0.02 | 1.2 (1.0, 1.5) | 71.4 | 0.19 | 2.4 (2.0, 3.0) |
1e-5 (ORS) | 126 | 69.4 | 0.16 | 2.2 (1.8, 2.7) | 66 | 56.7 | 0.02 | 1.2 (1.1, 1.5) | 72.0 | 0.20 | 2.4 (2.0, 3.0) |
0.1 | 68,681 | 64.9 | 0.09 | 1.8 (1.5, 2.2) | 68,516 | 61.3 | 0.06 | 1.6 (1.3, 1.9) | 74.1 | 0.24 | 2.8 (2.2, 3.4) |
0.5 | 203,950 | 62.6 | 0.07 | 1.7 (1.4, 2.0) | 203,710 | 60.5 | 0.05 | 1.5 (1.3, 1.8) | 73.7 | 0.23 | 2.7 (2.2, 3.4) |
Legend: PRSs were calculated on a case-control cohort (271 clinically defined AD cases and 278 cognitively normal controls) using Kunkle et al. (2019) summary statistics for pT ≤ 5e-8, 1e-5, 0.1, 0.5 LD-pruned SNPs and APOE(ε2 + ε4). The number of SNPs (NSNPs) in each risk score are reported. Three PRS models were considered: PRS.full calculated on the full summary statistics; PRS.no.APOE where the APOE region was excluded (chr19:44.4–46.5 Mb); PRS.AD which is calculated as a weighted sum of PRS.no.APOE and APOE(ε2 + ε4), where APOE effects were weighted with effect sizes (B(ε2) = −0.47 and B(ε4) = 1.12) as in Kunkle et al (2019). The number of SNPs for PRS.AD models is always two more than for PRS.no.APOE. Prediction was estimated in terms of AUC, R2 and OR with 95% Confidence Intervals (CI).